Defining and targeting epigenetic plasticity-driven drug resistance and immune escape in melanoma

定义和针对黑色素瘤中表观遗传可塑性驱动的耐药性和免疫逃逸

• 批准号: 10666665
• 负责人: Jonathan D. Licht
• 金额: $ 47.85万
• 依托单位: H. LEE MOFFITT CANCER CTR & RES INST
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-15 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10666665
• 关键词: 3-Dimensional; ATAC-seq; Acetylation; Address; Affect; Antigen Presentation; Antigens; BRAF gene; CD8-Positive T-Lymphocytes; CRISPR screen; Cell Line; Cell Lineage; Cells; Chromatin; Chromatin Loop; Clinical; Clinical Trials; Complex; Data; Deacetylation; Development; Drug resistance; EP300 gene; Environment; Enzymes; Epidermal Growth Factor Receptor; Epigenetic Process; Excision; Exclusion; Future; Gene Expression; Genes; Genetic Transcription; Grant; HDAC8 gene; Hi-C; Histocompatibility Antigens Class I; Histone Deacetylase; Histone Deacetylase Inhibitor; Immune; Immune Evasion; Immune checkpoint inhibitor; Immune system; Immunosuppression; Immunotherapy; In Vitro; Interferons; Interleukin-11; MEKs; Mediating; Melanoma Cell; Mesenchymal; Modeling; Mus; Mutation; Myelogenous; PTEN gene; Pathway interactions; Pharmaceutical Preparations; Phenotype; Prevention; Proteins; Proteomics; Resistance; Role; Signal Transduction; Signaling Protein; Specimen; T cell infiltration; T-Lymphocyte; Testing; Transcription Factor AP-1; Work; cancer type; checkpoint therapy; cofactor; cohesin; drug maintenance; drug withdrawal; immune checkpoint; immunoregulation; improved; in vivo; inhibitor; inhibitor therapy; insight; jun Oncogene; loss of function; melanoma; mouse model; multiple omics; novel; novel therapeutic intervention; novel therapeutics; overexpression; prevent; programs; recruit; response; sample fixation; single-cell RNA sequencing; small molecule inhibitor; targeted treatment; therapy resistant; transcription factor; treatment response; tumor; tumor eradication; tumor-immune system interactions

Project summary Melanoma is a heterogeneous tumor, with a high degree of phenotypic plasticity that allows for rapid adaptation to BRAF-MEK inhibitor therapy. Initial therapeutic responses are typically followed by a period of quiescence in which signaling is rewired to evade therapy, followed by the emergence of a bona fide resistant state. Little is known about how the initial persister cell state transitions to an irreversibly resistant state, the role of the immune system in the emergence of these lineages, and whether this resistant state can be targeted. In preliminary studies we identified the type I histone deacetylase HDAC8 as a master regulator of a lineage switch to a resistance-associated melanoma cell state. Activation of HDAC8 alters the phenotype of melanoma cells with loss of function of lineage identity genes such as MITF, increased activity of AP-1/TEAD transcription factors and resistance to therapy. The resistant cell state persisted even after removal of targeted therapy, and was associated with increased mutational load. HDAC8 overexpression also led to the reduced expression of melanoma antigens, increased levels of the immune checkpoint proteins and reduced T cell infiltration. We believe the stability of this state may be at least in part be epigenetic due to altered acetylation and function of transcription factors, cofactors as well as altered function of the cohesin complex involved in chromatin looping, and gene expression. We hypothesize that HDAC8 is a master regulator of a resistance-associated melanoma cell state and represents a target for the prevention of lineage switching. In this proposal, we will use multi-omics approaches (ATAC-Seq, scRNA-Seq, Hi-C, proteomics) to define the mechanisms by which HDAC8 reprograms melanoma cells, and will determine if HDAC8 affects the cohesin complex, leading to fixed resistance-conferring genetic or epigenetic changes. We will utilize a mouse model of BRAF/PTEN-HDAC8-driven melanoma and single cell RNA-Seq to investigate how the HDAC8 modulates the immune microenvironment leading to the emergence of drug resistant melanoma lineages. We will specifically determine whether HDAC8 drives a transcriptional program associated with decreased MHC class I and antigen expression leading to decreased tumor-T cell recognition. Further studies will define whether JUN-mediated transcription of IL-11 reprograms the myeloid compartment leading to a suppressive melanoma immune environment that eradicates tumor-reactive CD8 T cells. CRISPR screens will be performed to identify targets to prevent the emergence of drug resistant lineages in mouse models. We will then evaluate these targets and HDAC8 inhibitors as strategies to improve therapeutic responses to BRAF-MEK inhibitor and immune checkpoint inhibitor therapy in syngeneic mouse melanoma models. We expect that new insights into the mechanisms underpinning the emergence and maintenance of drug resistant lineages in melanoma will lead to the development of new therapeutic strategies to improve the depth and duration of responses to immunotherapy and targeted therapy in melanoma. Our findings will have important implications across multiple cancer types and many different therapies.

项目概要 黑色素瘤是一种异质性肿瘤，具有高度的表型可塑性，可以快速适应 BRAF-MEK 抑制剂治疗。最初的治疗反应之后通常是一段时间的静止期 该信号被重新连接以逃避治疗，随后出现真正的抵抗状态。小的是 了解最初的持久细胞状态如何转变为不可逆的抵抗状态，免疫的作用 系统中这些谱系的出现，以及这种抵抗状态是否可以被针对。在初步 在研究中，我们发现 I 型组蛋白脱乙酰酶 HDAC8 是谱系转换的主要调节因子。 耐药相关的黑色素瘤细胞状态。 HDAC8 的激活改变了黑色素瘤细胞的表型 MITF 等谱系识别基因功能丧失，AP-1/TEAD 转录因子活性增加 和对治疗的抵抗力。即使在取消靶向治疗后，耐药细胞状态仍持续存在，并且 与突变负荷增加有关。 HDAC8 过度表达也导致 黑色素瘤抗原、免疫检查点蛋白水平增加以及 T 细胞浸润减少。我们 相信这种状态的稳定性可能至少部分是由于乙酰化和功能的改变而导致的表观遗传 转录因子、辅因子以及参与染色质环化的粘连蛋白复合物的功能改变， 和基因表达。我们假设 HDAC8 是耐药相关黑色素瘤的主要调节因子 细胞状态并代表防止谱系转换的目标。在这个提案中，我们将使用多组学 方法（ATAC-Seq、scRNA-Seq、Hi-C、蛋白质组学）来定义 HDAC8 重编程机制 黑色素瘤细胞，并将确定 HDAC8 是否影响粘连蛋白复合物，从而导致固定的抗性赋予 遗传或表观遗传变化。我们将利用 BRAF/PTEN-HDAC8 驱动的黑色素瘤小鼠模型 单细胞 RNA-Seq 研究 HDAC8 如何调节免疫微环境，从而导致 耐药黑色素瘤谱系的出现。我们将具体确定 HDAC8 是否驱动 与 MHC I 类和抗原表达减少相关的转录程序，导致 肿瘤T细胞识别。进一步的研究将确定 JUN 介导的 IL-11 转录是否会重新编程 骨髓室形成抑制性黑色素瘤免疫环境，消除肿瘤反应性 CD8 T 细胞。将进行 CRISPR 筛选以确定靶点以防止出现耐药性 小鼠模型中的谱系。然后我们将评估这些靶点和 HDAC8 抑制剂作为改善策略 同基因小鼠对 BRAF-MEK 抑制剂和免疫检查点抑制剂治疗的治疗反应 黑色素瘤模型。我们期望对支撑其出现和发展的机制有新的见解 黑色素瘤耐药谱系的维持将导致新治疗策略的开发 提高黑色素瘤免疫治疗和靶向治疗反应的深度和持续时间。我们的 研究结果将对多种癌症类型和许多不同的疗法产生重要影响。